Upgrade plugins and to Grails 2.3.0; use aether
Detect incomplete configurations loaded

We know have a magic setting, org.transmart.configFine, which must be
Boolean.TRUE for tranSMART to accept running.

The reason for this is that if the file ~/.grails/transmartConfig has
errors, grails will ignore those errors and continue. The Grails code
indicates tries to log a WARN, but this happens apparently too early
in the boot process and and the logger it uses seems a) to have
onlu a null appender attached and b) its minimum error level is ERROR
anyway.

By placing this property at the very end of the Config.groovy file, we
can be sure that the configuration was completely run.

Conflicts:
	grails-app/conf/BootStrap.groovy
Improve conf error message on Bootstrap

Mention the console logging settings can be changed by editiing
$GRAILS_HOME/scripts/log4j.properties.
Change app name; change out-of-tree conf files loc

From ~/.grails/transmartAppConfig to
~/.grails/transmartConfig
Deprecate RModulesConfig.groovy
Improve Config.groovy

This commit includes two changes:
* Make the binding used to run grails-app/conf/Config.groovy available
  to the externalized Config.groovy
  (~/.grails/transmartConfig/Config.groovy). See the comment in the code
  for the rationale.
* Remove some configuration relative to spring security since, for
  better or worse, that was moved to the externalized file.

Conflicts:
	grails-app/conf/Config.groovy
Remove DataSourcePlaceHolder
Allow disabling spnego authentication

Made it disabled by default.

Controlled by the setting: org.transmart.security.spnegoEnabled
Bugfix for Jira item THRONE-50: Download Exported Job fails

Conflicts:
	grails-app/services/com/recomdata/transmart/data/export/PostgresExportService.groovy
Updating ehcache configuration to fix grails 2.x loaing warning.
Reduce log statement severity
Reduce log statement severity
Out-of-tree in-line plugin conf/repos from master
Remove a few libs from lib/; some added to BuildConfig
Error rendering improvement

Conflicts:
	web-app/css/errors.css
Add prototype plugin; remove prototype files
Fix deapp not loading
Add dependencies on core-api and core-db

Conflicts:
	grails-app/conf/BuildConfig.groovy
Remove dev env data source configuration

This must come from the out-of-tree
~/.grails/transmartConfig/DataSource.groovy file

Conflicts:
	grails-app/conf/DataSource.groovy
Use db-core's getCategories instead of i2b2's

Conflicts:
	web-app/js/datasetExplorer/datasetExplorer.js
	web-app/js/datasetExplorer/requests.js